Please go to the following link with 2 cubes printed before and after I changed the drivers. Easy to spot which is the one printed before and after
There are still some issues I haven't tweaked yet, like ghosting and wrapping, but those are relatively easy to fix.

Yeah, I know it's a shame and I'm quite frustrated with the output quality of this printer.
Yes, I did all the things recommended on that document, and much more, like replacing all the linear bearings, replacing the hotends, the threaded rods, reprint some parts, etc.
Right now I'm tweaking with the firmware settings trying to improve something more.

to solve Z axis problems with the original rods the best solutions I found are:
-Lube the threaded rods very very well, I use lithium grease, beware it is messy and turns dark/geyish quite fast with consistent use
-Make sure the brass nuts are completely still on the X gantry, if they spin even the slightest you will have issues
-Make sure you have the couplers correctly installed, 5mm inserted on each side and the middle (springy part) without anything to allow it to compensate some misalignment due to the bend of the threaded rods
-Run up and down the Z axes a couple of times to allow the lube to properly propagate
-Reduce the Z axis speed to 2 on the printer menu on "Control" > "Motion" > "Velocity" > "Z axis", alternatively add "M203 Z2" to the start Gcode
-Decrease the Z axis acceleration to 50-100 on "Control" > "Motion" > "Acceleration" > "Z axis", alternatively add "M201 Z50" to the start Gcode

Other than that you can change the threaded rods to 5mm trapezoidal rods and that make quite a difference vs the default one out of the box (albeit if you follow the previous advises it should have similar results) but you need to customize some parts to allow the insertion of the new trapezoidal nuts.

As for the ghosting, lower the print speed and acceleration, for warping clean the glass very well with window cleaner until it squeaks when rubbing, prior to printing.

Hello...i think the lines on the firmware are self explanatory, you uncomment the first one if you want the TMC2208 on the extruder only or the second line if you replace all 5 stepper drivers. Other than that you just need to change the stepper drivers themselves